Mitotic recombinatory evolution in acute leukemia.

A cohort of leukemia cases is presented with ancillary testing that includes microarray studies, karyotyping, FISH, and RNA sequencing to illustrate clonal evolution. Common evolution etiology with each case is apparent homologous mitotic recombination (HMR). The cohort includes: four cases of Pre B-cell acute lymphoblastic leukemia (B-ALL) with a single translocation derivative (19)t(1;19)(q23.3;p13.3), an acute myelogenous leukemia (AML) case with a paracentric inversion of 11q13.3q23 in both homologues confirmed as a rare KMT2A-MAML2 gene fusion, and a transplant patient in AML relapse with a t(6;11)(6q27;q23) and evolution to an additional derivative 6 chromosome. The PBX1-TCF3 fusion in the t(1;19) B-ALL subgroup has long been associated with clones that show either the balanced translocation (∼25%) or the unbalanced single derivative 19 (∼75%).  Evidence from the CMAs and FISH is consistent with HMR initiating at either the PBX1 translocation breakpoint or at a more proximal long arm site that mediates the evolution to the unbalanced form. This is contrary to the previous assumptions of either nondisjunction duplication of the normal homologue with loss of the translocation derivative 1 or an original trisomy 1 that loses the translocation derivative 1. Relapse from an unrelated transplant donor created unique allele dosage ratios in the microarray of the AML patient with the t(6;11) KMT2A-AFDN fusion.  An HMR-based evolution initiation site proximal to the 6q27 AFDN fusion gene is evident in the microarray of chromosome 6, the known oncogenic fusion derivative. The HMR selection driver in both AML cases is very likely associated with the DNA doubling of the oncogenic fusions in 6q and 11q, respectively. Since the oncogenic derivatives in the 1;19 cases are clearly the retained derivative 19, selection for the HMR clonal evolution in 1q is apparently based on the known proliferative advantage of extra copies of 1q in B-ALL and other malignancies. Although selection-based HMR can effectively initiate at any site proximal to a driver gene fusion, it appears that the translocation breaksite is common for many translocations. In addition, evidence from HMR evolution related distal 11q mutations, numerous unbalanced CCND1/IGH translocations, and the double MAML2/KMT2A presented in this study suggest that a recombinatorial "hot spot" exists near the CCND1 gene in many rearrangements or mutations within 11q.

Clinical significance and mechanisms associated with segmental UPD.

Whole chromosome uniparental disomy (UPD) has been well documented with mechanisms largely understood. However, the etiology of segmental limited UPD (segUPD) is not as clear. In a 10-year period of confirming (> 300) cases of whole chromosome UPD, we identified 86 segmental cases in both prenatal and postnatal samples. Thirty-two of these cases showed mosaic segmental UPD at 11p due to somatic selection associated with Beckwith-Wiedemann syndrome. This study focuses on apparent mechanisms associated with the remaining cases, many of which appear to represent corrections of genomic imbalance such as deletions and derivative chromosomes. In some cases, segmental UPD was associated with the generation of additional genomic imbalance while in others it apparently resulted in restoration of euploidy. Multiple tests utilizing noninvasive prenatal testing (NIPT), chorionic villus sampling (CVS) and amniotic fluid samples from the same pregnancy revealed temporal evidence of correction and a "hotspot" at 1p. Although in many cases the genomic imbalance was dosage "repaired" in the analyzed tissue, clinical effects could be sustained due to early developmental effects of the original imbalance or due to its continued existence in other tissues. In addition, if correction did not occur in the gametes there would be recurrence risks for the offspring of those individuals. Familial microarray allele patterns are presented that differentiate lack of gamete correction from somatic derived gonadal mosaicism. These results suggest that the incidence of segUPD mediated correction is underestimated and may explain the etiology of some clinical phenotypes which are undetected by routine microarray analysis and many exome sequencing studies.

Multidisciplinary analysis of pediatric T-ALL: 9q34 gene fusions.

T-cell acute lymphoblastic leukemia (T-ALL) is not as frequently reported as the B-cell counterpart (B-ALL), only occurring in about 15% of pediatric cases with a typically heterogeneous etiology. Approximately 8% of childhood T-ALL cases have rearrangements involving the ABL1 tyrosine kinase gene at 9q34.12; although a t(9;22), resulting in a fusion of ABL1 with the BCR gene at 22q11.23 is a common occurrence in B-ALL, it is not a typical finding in T-ALL. A subset of 10 of 40 documented cases of T-ALL analyzed over a 5-year period is presented, each having gene rearrangements within band 9q34 that resulted in fusions other than BCR/ABL1. These cases included fusions involving ABL1, SET (9q34.11), NUP214 (9q34.13), SPTAN1 (9p34.11), and TNRC6B (22q13.1). Among the 10 cases are: six SET/NUP214 fusions, two ABL1/NUP214 fusions (one of which was associated with episomal amplification) and novel SPTAN1/ABL1 and TNRC6B/ABL1 fusions. The evaluations of these clones were each significantly aided by FISH analysis, which directed subsequent microarray and anchored multiplex PCR testing for fusion confirmations.

Four-copy number intervals in SNP microarray analysis: unique patterns and positions.

Over the past several years, the utility of microarray technology in delineating copy number changes has become well established. In the past 4 years, we have used the SNP array to detect and analyze allele ratios in 150 cases with 4-copy intervals, confirmed by FISH, offering insight into the underlying mechanisms of formation. These cases may be divided into 5 allele patterns--the first 4 of which involve a single homologue--as detected by the genotyping aspects of the microarray: (1) triplications combining homozygous and heterozygous alleles, with a 3:1 ratio of heterozygotes; (2) triplications with allele patterns combining homozygous and heterozygous alleles, with heterozygote ratios of both 3:1 and 2:2; (3) triplications that have homozygous alleles combined with only 2:2 heterozygous alleles; (4) triplications that are completely homozygous; and (5) homozygous duplications on each homologue with no heterozygous alleles. The implications of copy number variants with diverse allelic segregations are presented in this study.